For many decades, gel electrophoresis has been the preferred method for the separation and characterization of nucleic acids. The imaging of nucleic acids within these gels is currently possible via small molecule staining agents, which provide a measureable colocalized response. Nucleic acid stains typically possess planar, conjugated π systems with excited-state photophysical properties, which allows them to be visualized using fluorescence gel plate readers. The sensitivity of these methods relies on structures that luminesce in a nucleic acid environment but are quenched by the surrounding hydrogel matrix, thus reducing the overall background signal. Although it is possible to perform gel electrophoresis under denaturing conditions in order to remove the presence of base-pairing and other intramolecular interactions, running the gel under conditions that support hybridization to distinguish single-stranded DNA (ssDNA) from its duplex state could provide additional useful information regarding the structural state of the nucleic acids. Such information would be particularly helpful in applications which rely on differentiating the amount of double stranded DNA (dsDNA) from ssDNA, such as the DNA amplification step involved in polymerase chain reactions (PCR). To date, identifying molecules that exhibit specific interactions for dsDNA rather than ssDNA, both in solution and within gel electrophoresis assays, remains a challenge.